Unraveling Nitrogen Cycling by Soil Microbes

The Science

Large amounts of nitrogen enter soil ecosystems as nitrate (NO3) fertilizers. In addition to being available as a nitrogen source, a variety of soil microbes can generate energy from NO3 either by (1) denitrification, the conversion of NO3 to ammonia (NH4+), or (2) respiratory ammonification, which results in a mixture of nitrous oxide and dinitrogen gas (N2O and N2). NH4+ remains in soil while N2O and N2 are lost to the atmosphere, where N2O acts as a potent greenhouse gas. Understanding the microorganisms that perform these competing pathways is important for both agriculture and global climate change. Researchers at the University of Tennessee and Oak Ridge National Laboratory examined the systems biology properties of an unusual microbe able to perform both of these processes. While the majority of microbes utilizing NO3 as an energy source perform either denitrification or ammonification, the bacterium Shewanella loihica was shown to possess both pathways and thus offers a unique opportunity to examine the specific environmental factors that result in production of NH4+ versus N2O and N2. Using a series of careful physiological studies coupled to measurements of gene expression, the team determined that S. loihica activates the most energetically favorable pathway depending on its growth conditions, with the ratio of available carbon substrates to nitrogen availability (C/N ratio) playing the most influential role in the organism opting for either ammonification or denitrification. Recent studies have shown that organisms like S. loihica that are capable of both denitrification and ammonification are far more common in soil ecosystems than previously suspected. As such, this study’s findings have major implications for predicting climate change impacts on terrestrial biogeochemical cycles and designing more sustainable bioenergy agriculture practices.

Principal Investigator

Frank E. Löffler
University of Tennessee–Knoxville

BER Program Manager

Dawn Adin

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Yoon, S., C. Cruz-Garcia, R. Sanford, K. M. Ritalahti, and F. E. Loffler. 2014. “Denitrification Versus Respiratory Ammonification: Environmental Controls of Two Competing Dissimilatory NO3/NO2 Reduction Pathways in Shewanella loihica Strain PV-4,” The ISME Journal, DOI: 10.1038/ismej.2014.201.